Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25324.34 
• Atom Count: 1751 
• Residue Count: 179 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

1CW0

CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DNA

• DOI: 10.2210/pdb1CW0/pdb
• NDB: PD0100

• Classification: HYDROLASE/DNA
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli


• Deposited: 1999-08-25 Released: 1999-12-12 
• Deposition Author(s): Tsutakawa, S.E., Jingami, H., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.230 
• R-Value Work: 0.204 

Literature

Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex.

Tsutakawa, S.E., Jingami, H., Morikawa, K.

(1999) Cell 99: 615-623

• PubMed: 10612397 


• PubMed Abstract: 
  

The crystal structure of very short patch repair (Vsr) endonuclease, in complex with Mg2+ and with duplex DNA containing a TG mismatch, has been determined at 2.3 A resolution. In E. coli, the enzyme recognizes a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine. Extensive interactions between the DNA and the protein characterize a novel recognition mechanism, where three aromatic residues intercalate from the major groove into the DNA to strikingly deform the base pair stacking. With the presence of a cleaved DNA intermediate in the active center, the structure of the Vsr/DNA complex provides detailed insights into the catalytic mechanism for endonuclease activity.

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Organizational Affiliation: 

Department of Structural Biology, Biomolecular Engineering Research Institute, Suita, Osaka, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (DNA MISMATCH ENDONUCLEASE)	A	155	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: vsr EC: 3.1.-.-
Find proteins for P09184 (Escherichia coli (strain K12)) Go to UniProtKB:  P09184

Entity ID: 1
Molecule	Chains	Length	Organism
DNA (5'-D(*AP*CP*GP*TP*AP*CP*CP*TP*GP*GP*CP*T)-3')	M	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(*AP*GP*C)-3')	N	3	N/A

Entity ID: 3
Molecule	Chains	Length	Organism
DNA (5'-D(P*TP*AP*GP*GP*TP*AP*CP*GP*T)-3')	O	9	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	A, N	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.230 
• R-Value Work: 0.204 
• Space Group: P 6₅

Unit Cell:

Length (Å)	Angle (°)
a = 63.000	α = 90.00
b = 63.000	β = 90.00
c = 152.500	γ = 120.00

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
SCALEPACK	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-08-25 
• Released Date: 1999-12-12 
• Deposition Author(s): Tsutakawa, S.E., Jingami, H., Morikawa, K.

Revision History 

• Version 1.0: 1999-12-12
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance